Jiang Liang

In silico identification of silkworm selenoproteomes

Selenium (Se) is an essential trace element in vivo. Its biological function is mainly exerted through selenoproteins. Selenocysteine (Sec), the active site of selenoproteins, is incorporated into the protein at an in-frame TGA codon under the guidance of Sec insertion sequence (SECIS) element in the 3′-untranslated region (UTR) of the gene. In this work, a method was developed and a series of programs were edited by PERL language to in silico identify selenoproteomes from the genome of domesticated silkworm (Bombyx mori). Out of 18510 annotated genes, 6348 was terminated with TGA codons, 249 containing both in-frame TGAs and SECIS elements in the 3′-UTRs. Alignments of those selenoprotein candidates with their cysteine (Cys)-containing homologs revealed that 52 genes had TGA/Cys pairs and similar flanking regions around the in-frame TGAs. Restricted by the pattems of SECIS elements only 5 genes were screened out to fully meet the requirements for selenoproteins. Among them glutathione S-transferase (GST) has been reported as a microbial selenoprotein, the other four are novel selenoproteins annotated as CG6024, CG5195, ATP-binding cassette transporter subfamily A (ABCA), and nuclear VCP-like protein. Derived from the general properties of GST, ABCA and VCP, silkworm selenoproteins may play important roles in redox regulation, Se storage and transportation, as well as cell apoptosis.

New Selenoproteins Identified in silico from the Genome of Anopheles gambiae

Selenoprotein is biosynthesized by the incorporation of selenocysteine into proteins, where the TGA codon in the open reading frame does not act as a stop signal but is translated into selenocysteine. The dual functions of TGA result in mis-annotation or lack of selenoproteins in the sequenced genomes of many species. Available computational tools fail to correctly predict selenoproteins. Thus, we developed a new method to identify selenoproteins from the genome of Anopheles gambiae computationally. Based on released genomic information, several programs were edited with PERL language to identify selenocysteine insertion sequence (SECIS) element, the coding potential of TGA codons, and cysteine-containing homologs of selenoprotein genes. Our results showed that 11365 genes were terminated with TGA codons, 918 of which contained SECIS elements. Similarity search revealed that 58 genes contained Sec/Cys pairs and similar flanking regions around in-frame TGA codons. Finally, 7 genes were found to fully meet requirements for selenoproteins, although they have not been annotated as selenoproteins in NCBI databases. Deduced from their basic properties, the newly found selenoproteins in the genome of Anopheles gambiae are possibly related to in vivo oxidation tolerance and protein regulation in order to interfere with anopheles’ vectorial capacity of Plasmodium. This study may also provide theoretical bases for the prevention of malaria from anopheles transmission.